Path Integral Method for DNA Denaturation

Abstract

The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the second law of thermodynamics. The number of paths contributing to the partition function strongly increases around and above a specific temperature $T_c^{\ast }$ whereas the fraction of unbound base pairs grows continuosly around and above $T_c^{\ast }$. The latter is identified with the denaturation temperature. Thus, the separation of the two complementary strands appears as a highly cooperative phenomenon displaying a smooth crossover versus $T$. The thermodynamical properties have been computed in a large temperature range by varying the size of the path ensemble at the lower bound of the range. No significant physical dependence on the system size has been envisaged. The entropy grows continuosly versus $T$ while the specific heat displays a remarkable peak at $T_c^{\ast }$. The location of the peak versus $T$ varies with the stiffness of the anharmonic stacking interaction along the strand. The presented results suggest that denaturation in homogeneous DNA has the features of a second order phase transition. The method accounts for the cooperative behavior of a very large number of degrees of freedom while the computation time is kept within a reasonable limit.

Physical Review E 2009 in press

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Cited by in corpus (22)

• Thermodynamics of Twisted DNA with Solvent Interaction
• Denaturation Patterns in Heterogeneous DNA
• Stacking Interactions in Denaturation of DNA Fragments
• Twist versus Nonlinear Stacking in Short DNA Molecules
• Helix untwisting and bubble formation in circular DNA
• End-to-end distance and contour length distribution functions of DNA helices
• Flexibility of short DNA helices under mechanical stretching
• Entropic Penalties in Circular DNA Assembly
• Theoretical and Experimental Investigations of DNA Open States
• Anharmonic oscillation effect on the Davydov-Scott monomer in thermal bath
• Twisting short dsDNA with applied tension
• Investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method
• Anharmonic stacking in supercoiled DNA
• First-passage probability: a test for DNA Hamiltonian parameters
• Twist-stretch profiles of DNA chains
• Renormalisation group determination of the order of the DNA denaturation transition
• Mesoscopic helical models for DNA
• Modeling DNA Dynamics by Path Integrals
• Unwinding of circular helicoidal molecules versus size
• Helical Disruptions in Small Loops of DNA
• Mesoscopic model for nano-channel confined DNA
• Statistical method for A-RNA and B-DNA